A 6D structure model for face-centred icosahedral quasicrystals consisting of so-called pseudo-Mackay and mini-Bergman-type atomic clusters is proposed based on the structure model of the Al69.1Pd22Cr2.1Fe6.8 3/2 cubic approximant crystal (with space group Pa3, a = 40.5 Å) [Fujita et al. (2013). Acta Cryst. A69, 322-340]. The cluster centres form an icosahedral close sphere packing generated by the occupation domains similar to those in the model proposed by Katz & Gratias [J. Non-Cryst. Solids (1993), 153-154, 187-195], but their size is smaller by a factor τ2 [τ = (1 + (5)1/2)/2]. The clusters cover approximately 99.46% of the atomic structure, and the cluster arrangement exhibits 15 and 19 different local configurations, respectively, for the pseudo-Mackay and mini-Bergman-type clusters. The occupation domains that generate cluster shells are modelled and discussed in terms of structural disorder and local reorganization of the cluster arrangements (phason flip).
{"title":"Structure of face-centred icosahedral quasicrystals with cluster close packing.","authors":"Tsunetomo Yamada, Hiroyuki Takakura, Akiji Yamamoto","doi":"10.1107/S2053273324008568","DOIUrl":"10.1107/S2053273324008568","url":null,"abstract":"<p><p>A 6D structure model for face-centred icosahedral quasicrystals consisting of so-called pseudo-Mackay and mini-Bergman-type atomic clusters is proposed based on the structure model of the Al<sub>69.1</sub>Pd<sub>22</sub>Cr<sub>2.1</sub>Fe<sub>6.8</sub> 3/2 cubic approximant crystal (with space group Pa3, a = 40.5 Å) [Fujita et al. (2013). Acta Cryst. A69, 322-340]. The cluster centres form an icosahedral close sphere packing generated by the occupation domains similar to those in the model proposed by Katz & Gratias [J. Non-Cryst. Solids (1993), 153-154, 187-195], but their size is smaller by a factor τ<sup>2</sup> [τ = (1 + (5)<sup>1/2</sup>)/2]. The clusters cover approximately 99.46% of the atomic structure, and the cluster arrangement exhibits 15 and 19 different local configurations, respectively, for the pseudo-Mackay and mini-Bergman-type clusters. The occupation domains that generate cluster shells are modelled and discussed in terms of structural disorder and local reorganization of the cluster arrangements (phason flip).</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"422-438"},"PeriodicalIF":1.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142337536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-21DOI: 10.1107/S2053273324009550
Budhika G Mendis
In electron microscopy the principle of reciprocity is often used to imply time reversal symmetry. While this is true for elastic scattering, its applicability to inelastic scattering is less well established. From the second law of thermodynamics, the entropy for a thermally isolated system must be constant for any reversible process. Using entropy and statistical fluctuation arguments, it is shown that, while reversibility is possible at the microscopic level, it becomes statistically less likely for higher energy transfers. The implications for reciprocal imaging modes, including energy loss and energy gain measurements, as well as Kainuma's reciprocal wave model are also discussed.
{"title":"On the principle of reciprocity in inelastic electron scattering.","authors":"Budhika G Mendis","doi":"10.1107/S2053273324009550","DOIUrl":"10.1107/S2053273324009550","url":null,"abstract":"<p><p>In electron microscopy the principle of reciprocity is often used to imply time reversal symmetry. While this is true for elastic scattering, its applicability to inelastic scattering is less well established. From the second law of thermodynamics, the entropy for a thermally isolated system must be constant for any reversible process. Using entropy and statistical fluctuation arguments, it is shown that, while reversibility is possible at the microscopic level, it becomes statistically less likely for higher energy transfers. The implications for reciprocal imaging modes, including energy loss and energy gain measurements, as well as Kainuma's reciprocal wave model are also discussed.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"457-459"},"PeriodicalIF":1.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-09-23DOI: 10.1107/S2053273324007988
Nicolas Monge, Massih Reza Amini, Alexis Deschamps
Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202-212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.
{"title":"Influence of device configuration and noise on a machine learning predictor for the selection of nanoparticle small-angle X-ray scattering models.","authors":"Nicolas Monge, Massih Reza Amini, Alexis Deschamps","doi":"10.1107/S2053273324007988","DOIUrl":"10.1107/S2053273324007988","url":null,"abstract":"<p><p>Small-angle X-ray scattering (SAXS) is a widely used method for nanoparticle characterization. A common approach to analysing nanoparticles in solution by SAXS involves fitting the curve using a parametric model that relates real-space parameters, such as nanoparticle size and electron density, to intensity values in reciprocal space. Selecting the optimal model is a crucial step in terms of analysis quality and can be time-consuming and complex. Several studies have proposed effective methods, based on machine learning, to automate the model selection step. Deploying these methods in software intended for both researchers and industry raises several issues. The diversity of SAXS instrumentation requires assessment of the robustness of these methods on data from various machine configurations, involving significant variations in the q-space ranges and highly variable signal-to-noise ratios (SNR) from one data set to another. In the case of laboratory instrumentation, data acquisition can be time-consuming and there is no universal criterion for defining an optimal acquisition time. This paper presents an approach that revisits the nanoparticle model selection method proposed by Monge et al. [Acta Cryst. (2024), A80, 202-212], evaluating and enhancing its robustness on data from device configurations not seen during training, by expanding the data set used for training. The influence of SNR on predictor robustness is then assessed, improved, and used to propose a stopping criterion for optimizing the trade-off between exposure time and data quality.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"405-413"},"PeriodicalIF":1.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-08DOI: 10.1107/S2053273324008945
Craig S Kaplan, Michael O'Keeffe, Michael M J Treacy
This article describes the diffraction pattern (2-periodic Fourier transform) from the vertices of a large patch of the recently discovered `Spectre' tiling - a strictly chiral aperiodic monotile. It was reported recently that the diffraction pattern of the related weakly chiral aperiodic `Hat' monotile was 2-periodic with chiral plane-group symmetry p6 [Kaplan et al. (2024). Acta Cryst. A80, 72-78]. The diffraction periodicity arises because the Hat tiling is a systematic aperiodic deletion of vertices from the 2-periodic hexagonal mta tiling. Despite the similarity of the Hat and Spectre tilings, the Spectre tiling is not aligned with a 2-periodic lattice, and its diffraction pattern is non-periodic with chiral point symmetry 6 about the origin.
{"title":"Periodic diffraction from an aperiodic monohedral tiling - the Spectre tiling. Addendum.","authors":"Craig S Kaplan, Michael O'Keeffe, Michael M J Treacy","doi":"10.1107/S2053273324008945","DOIUrl":"10.1107/S2053273324008945","url":null,"abstract":"<p><p>This article describes the diffraction pattern (2-periodic Fourier transform) from the vertices of a large patch of the recently discovered `Spectre' tiling - a strictly chiral aperiodic monotile. It was reported recently that the diffraction pattern of the related weakly chiral aperiodic `Hat' monotile was 2-periodic with chiral plane-group symmetry p6 [Kaplan et al. (2024). Acta Cryst. A80, 72-78]. The diffraction periodicity arises because the Hat tiling is a systematic aperiodic deletion of vertices from the 2-periodic hexagonal mta tiling. Despite the similarity of the Hat and Spectre tilings, the Spectre tiling is not aligned with a 2-periodic lattice, and its diffraction pattern is non-periodic with chiral point symmetry 6 about the origin.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"460-463"},"PeriodicalIF":1.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01Epub Date: 2024-10-14DOI: 10.1107/S2053273324009008
Alexander P Shevchenko, Vladislav A Blatov
The crystal structure uniformity is numerically estimated as the standard deviation of the crystal space quantizer 〈G3〉. This criterion has been applied to explore the uniformity of ionic sublattices in 21465 crystal structures of inorganic ionic compounds. In most cases, at least one kind of sublattice (whole ionic lattice, cationic or anionic sublattice) was found to be highly uniform with a small 〈G3〉 value. Non-uniform structures appeared to be either erroneous or essentially non-ionic. As a result, a set of uniformity criteria is proposed for the estimation of the stability of ionic crystal structures.
{"title":"Stability of inorganic ionic structures: the uniformity approach.","authors":"Alexander P Shevchenko, Vladislav A Blatov","doi":"10.1107/S2053273324009008","DOIUrl":"10.1107/S2053273324009008","url":null,"abstract":"<p><p>The crystal structure uniformity is numerically estimated as the standard deviation of the crystal space quantizer 〈G<sub>3</sub>〉. This criterion has been applied to explore the uniformity of ionic sublattices in 21465 crystal structures of inorganic ionic compounds. In most cases, at least one kind of sublattice (whole ionic lattice, cationic or anionic sublattice) was found to be highly uniform with a small 〈G<sub>3</sub>〉 value. Non-uniform structures appeared to be either erroneous or essentially non-ionic. As a result, a set of uniformity criteria is proposed for the estimation of the stability of ionic crystal structures.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"446-456"},"PeriodicalIF":1.9,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-07-26DOI: 10.1107/S2053273324007113
Richard Beanland, Robin Sjökvist
The superstructure spots that appear in diffraction patterns of tilted perovskites are well documented and easily calculated using crystallographic software. Here, by considering a distortion mode as a perturbation of the prototype perovskite structure, it is shown how the structure-factor equation yields Boolean conditions for the presence of superstructure reflections. This approach may have some advantages for the analysis of electron diffraction patterns of perovskites.
{"title":"Superstructure reflections in tilted perovskites.","authors":"Richard Beanland, Robin Sjökvist","doi":"10.1107/S2053273324007113","DOIUrl":"10.1107/S2053273324007113","url":null,"abstract":"<p><p>The superstructure spots that appear in diffraction patterns of tilted perovskites are well documented and easily calculated using crystallographic software. Here, by considering a distortion mode as a perturbation of the prototype perovskite structure, it is shown how the structure-factor equation yields Boolean conditions for the presence of superstructure reflections. This approach may have some advantages for the analysis of electron diffraction patterns of perovskites.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"387-390"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11363165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-07-29DOI: 10.1107/S2053273324005643
Agatha Kristel Abila, Ma Louise Antonette De Las Peñas, Mark Tomenes
An edge-n-coloring of a uniform tiling {cal T} is uniform if for any two vertices of {cal T} there is a symmetry of {cal T} that preserves the colors of the edges and maps one vertex onto the other. This paper gives a method based on group theory and color symmetry theory to arrive at uniform edge-n-colorings of uniform tilings. The method is applied to give a complete enumeration of uniform edge-n-colorings of the uniform tilings of the Euclidean plane, for which the results point to a total of 114 colorings, n = 1, 2, 3, 4, 5. Examples of uniform edge-n-colorings of tilings in the hyperbolic plane and two-dimensional sphere are also presented.
{"title":"On uniform edge-n-colorings of tilings.","authors":"Agatha Kristel Abila, Ma Louise Antonette De Las Peñas, Mark Tomenes","doi":"10.1107/S2053273324005643","DOIUrl":"10.1107/S2053273324005643","url":null,"abstract":"<p><p>An edge-n-coloring of a uniform tiling {cal T} is uniform if for any two vertices of {cal T} there is a symmetry of {cal T} that preserves the colors of the edges and maps one vertex onto the other. This paper gives a method based on group theory and color symmetry theory to arrive at uniform edge-n-colorings of uniform tilings. The method is applied to give a complete enumeration of uniform edge-n-colorings of the uniform tilings of the Euclidean plane, for which the results point to a total of 114 colorings, n = 1, 2, 3, 4, 5. Examples of uniform edge-n-colorings of tilings in the hyperbolic plane and two-dimensional sphere are also presented.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"367-378"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141786469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-07-15DOI: 10.1107/S2053273324006569
Dmitry Chernyshov, Kenneth P Marshall, Erlend Tiberg North, Chloe A Fuller, David S Wragg
The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB6 from measurements made in different-sized capillaries.
原子对分布函数(PDF)是材料结构的实空间表示。实验 PDF 是通过对可能有或可能没有布拉格衍射峰的总散射数据进行傅立叶变换获得的。根据所用衍射仪的基本物理参数来确定散射数据中的布拉格峰分辨率是行之有效的方法,但在从倒数空间到直接空间的傅立叶变换之后,这些贡献就很难确定了。从 X 射线衍射大面积探测器分辨率函数的现有定义出发,这种方法被扩展到直接空间。仪器参数对 PDF 峰值分辨率的影响以数学方式进行了阐述,然后通过建模和与在不同尺寸毛细管中测量的 LaB6 实验 PDF 的比较进行了研究。
{"title":"Instrumental broadening and the radial pair distribution function with 2D detectors.","authors":"Dmitry Chernyshov, Kenneth P Marshall, Erlend Tiberg North, Chloe A Fuller, David S Wragg","doi":"10.1107/S2053273324006569","DOIUrl":"10.1107/S2053273324006569","url":null,"abstract":"<p><p>The atomic pair distribution function (PDF) is a real-space representation of the structure of a material. Experimental PDFs are obtained using a Fourier transform from total scattering data which may or may not have Bragg diffraction peaks. The determination of Bragg peak resolution in scattering data from the fundamental physical parameters of the diffractometer used is well established, but after the Fourier transform from reciprocal to direct space, these contributions are harder to identify. Starting from an existing definition of the resolution function of large-area detectors for X-ray diffraction, this approach is expanded into direct space. The effect of instrumental parameters on PDF peak resolution is developed mathematically, then studied with modelling and comparison with experimental PDFs of LaB<sub>6</sub> from measurements made in different-sized capillaries.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"358-366"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11363166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141615347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01Epub Date: 2024-08-08DOI: 10.1107/S2053273324007253
Adam Morawiec
Neutron time-of-flight transmission spectra of mosaic crystals contain Bragg dips, i.e., minima at wavelengths corresponding to diffraction reflections. The positions of the dips are used for investigating crystal lattices. By rotating the sample around a fixed axis and recording a spectrum at each rotation step, the intensity of the transmitted beam is obtained as a function of the rotation angle and wavelength. The questions addressed in this article concern the determination of lattice parameters and orientations of centrosymmetric crystals from such data. It is shown that if the axis of sample rotation is inclined to the beam direction, the reflection positions unambiguously determine reciprocal-lattice vectors, which is not the case when the axis is perpendicular to the beam. Having a set of such vectors, one can compute the crystal orientation or lattice parameters using existing indexing software. The considerations are applicable to arbitrary Laue symmetry. The work contributes to the automation of the analysis of diffraction data obtained in the neutron imaging mode.
{"title":"Indexing neutron transmission spectra of a rotating crystal.","authors":"Adam Morawiec","doi":"10.1107/S2053273324007253","DOIUrl":"10.1107/S2053273324007253","url":null,"abstract":"<p><p>Neutron time-of-flight transmission spectra of mosaic crystals contain Bragg dips, i.e., minima at wavelengths corresponding to diffraction reflections. The positions of the dips are used for investigating crystal lattices. By rotating the sample around a fixed axis and recording a spectrum at each rotation step, the intensity of the transmitted beam is obtained as a function of the rotation angle and wavelength. The questions addressed in this article concern the determination of lattice parameters and orientations of centrosymmetric crystals from such data. It is shown that if the axis of sample rotation is inclined to the beam direction, the reflection positions unambiguously determine reciprocal-lattice vectors, which is not the case when the axis is perpendicular to the beam. Having a set of such vectors, one can compute the crystal orientation or lattice parameters using existing indexing software. The considerations are applicable to arbitrary Laue symmetry. The work contributes to the automation of the analysis of diffraction data obtained in the neutron imaging mode.</p>","PeriodicalId":106,"journal":{"name":"Acta Crystallographica Section A: Foundations and Advances","volume":" ","pages":"379-386"},"PeriodicalIF":1.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141900167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}